I analyzed some RNA-Seq data using the old Tuxedo pipeline (Tophat, Cufflinks and cimmeRbund), but learned that there is an improvisation to the tuxedo protocol, so I ran hisat2, but am constantly getting 0% alignment. Is there anything that I'm doing wrong? I'm posting my command below -
hisat2 -p 8 --dta -x ../../data/ref/hg38 -1 ../../data/fastq/BT474_38_1.fastq -2 ../../data/fastq/BT474_38_2.fastq -S ../../data/hisat/bt474/bt474.sam
This was the command I ran. I would also like to point out that
hisat2-build -p 8 -c ../../data/ref/hg38.fa ../../data/ref/hg38
took less than 5 seconds to run. Is that normal?